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Nikos Vakirlis

@vakirlis.bsky.social

G4 Group Leader at the Hellenic Pasteur Institute, Evolutionary Genomics Group. We study the evolution of novel genes and antimicrobial peptides. https://vakirlislab.com/

40 Posts161 Follower178 Folgt
John Lees@johnlees.bacpop.org · 3mo ago

New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

Embeddings of gene order from PanBART model
Sam Horsfield@samuelhorsfield.bsky.social · 3mo ago

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

Genome Biology and Evolution@genomebiolevol.bsky.social · 6mo ago

@ccasola.bsky.social, A. Owoyemi and @vakirlis.bsky.social test the hypothesis that many noncanonical proteins possess low stability in the cellular environment, finding that noncanonical proteins were enriched for degradation-related features. 🔗 doi.org/10.1093/gbe/evag009 #genome #evolution

Degradation Determinants Are Abundant in Human Noncanonical Proteins and Minor Annotated Isoforms

Abstract. The comprehensive characterization of human proteins, a key objective in contemporary biology, has been revolutionized by the identification of t

doi.org

Claire Patiou, PhD.@cpatiou.bsky.social · 7mo ago

🧬 What does the starting material from which genes could emerge #denovo look like? 🌱 We used #RiboSeq to investigate the landscape of translated de novo ORFs in 3 #Arabidopsis species, and how they might be linked to gene birth! 📝 Check out our preprint here: doi.org/10.1101/2025...

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

Ancestrally non-genic sequences are now widely recognized as potential reservoirs for the de novo emergence of new genes. Across clades, some de novo genes were proven to have substantial phenotypic effects, and to contribute to the emergence of novel biological functions. Yet, still very little is known about the starting material from which de novo genes emerge, especially in plants. To fill this gap, we generated Ribosome Profiling data from the closely related species Arabidopsis halleri, A. lyrata and A. thaliana and characterized genome-wide patterns of translation across them. Synteny analysis revealed 211 Open Reading Frames (ORFs) that have emerged de novo within the Arabidopsis genus and already exhibit signs of active translation. Most of these de novo translated ORFs were species- and even accession-specific, indicating their transient nature, with patterns of polymorphism consistent with neutral evolution in natural populations. They were also significantly shorter and less expressed than conserved Coding DNA Sequences (CDS), and their GC content increased with phylogenetic conservation. While most of them were located in intergenic regions and are thus newly discovered, 34 were previously annotated as CDS in at least one genome, and are promising putative genes. Our results demonstrate the abundance of translation events outside of conserved CDS, and their role as starting material for the emergence of novel genes in plants. ### Competing Interest Statement The authors have declared no competing interest. Université de Lille, https://ror.org/0546v5182

doi.org

Jonathan Pritchard@jkpritch.bsky.social · 2y ago

Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Human prehistory [separate thread] 3.4: Ancient DNA: a genetic time capsule [this thread] web.stanford.edu/group/pritch...

An Owner's Guide to the Human Genome

An Owner's Guide to the Human Genome

web.stanford.edu

Jonathan Pritchard@jkpritch.bsky.social · 3y ago

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

Genome Biology and Evolution@genomebiolevol.bsky.social · 7mo ago

@ccasola.bsky.social, V. Luria, @vakirlis.bsky.social & @lizhao.bsky.social discuss advances and open questions in de novo gene emergence and evolution presented at the SMBE Satellite Meeting on De Novo Gene Birth (@official-smbe.bsky.social). 🔗 doi.org/10.1093/gbe/evaf230 #genome #evolution

De Novo Genes: Current Status and Future Goals

Abstract. The recent Society for Molecular Biology and Evolution Satellite Meeting on De Novo Gene Birth, hosted at Texas A&M University on November 6

doi.org

Camille Berthelot@camilleberthelot.bsky.social · 8mo ago

New preprint from our lab, spearheaded by @maelledaunesse.bsky.social and in collaboration with Diego Villar! In which we ask, can we detect joint signatures suggestive of positive selection on transcriptomes and epigenomes?

Maëlle Daunesse@maelledaunesse.bsky.social · 8mo ago

We've just released our new preprint! 🐀✨ doi.org/10.1101/2025... How do gene expression and regulation evolve during adaptation? And how can we tell adaptive shifts apart from simple drift? @camilleberthelot.bsky.social 👇 A short thread on what we found in African mole-rats.

Nikos Vakirlis@vakirlis.bsky.social · 9mo ago

When I see someone trying to sell this shit I feel the urge to remind people of the "metaverse". Remember how it was the future of the internet 5 years ago? Meta alone has already lost $70B on this nonsense. Imagine how much good they could have done with that money. www.techbuzz.ai/articles/met...

Meta's Reality Labs burns $4.4B as VR bet hits $70B loss

Meta's metaverse division posts massive Q3 loss despite beating expectations

techbuzz.ai

derek guy@dieworkwear.bsky.social · 9mo ago

Why would someone pay $20k for a robot controlled by a human in a remote location to do things more slowly and clumsily when the median wage for a maid or housekeeper is $33k per year, which is typically spread across 10-20 households?

Arlin Stoltzfus@evolarlin.bsky.social · 10mo ago

our next evol-mut-circle seminar (21 Oct, 15:00 UTC) features Timothy Fuqua on "De novo promoters emerge more readily from random DNA than genomic DNA" www.biorxiv.org/content/10.1... DM me to join the email list. Full schedule: www.molevol.org/evol-mut-cir... #popgen, #mutation, #evobio

De-novo promoters emerge more readily from random DNA than from genomic DNA

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

biorxiv.org

Workshops@evomics.bsky.social · 10mo ago

The 2026 Workshop on Phylogenomics will take place between the 25th of January and 7th of February, in Cesky Krumlov, Czechia. 🧬🌳 Applications are now open! Deadline: 15th of November, 2025. Do not miss the chance to attend! Spread the word among colleagues! 🤗 evomics.org/apply-worksh...

RECOMB Conference Series@recombconf.bsky.social · 10mo ago

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date! Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

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